A Whole Different Story
by whatever-remains
Summary: "Doctor Molly Hooper was a perfectly normal English woman. It was just her human friends who were not-so-normal. But Sherlock Holmes, Consulting Detective, was a whole different story. However, the friendship between Molly and Sherlock would suddenly become tested, unknown to both parties involved." Post-Reichenbach, Sherlock/Molly John/Mary
1. Chapter 1

**Title:** A Whole Different Story

**Rating:** M

**Pairings:** Sherlock/Molly and John/Mary

**Warnings:** Strong implications of rape and some steamy scenes later.

**Summary:** Doctor Molly Hooper was a perfectly normal English woman. It was just her human friends who were not-so-normal. But Sherlock Holmes, Consulting Detective, was a whole different story. However, the friendship between Molly and Sherlock would suddenly become tested, unknown to both parties involved.

**Disclaimer:** The characters are the brainchild of Sir Arthur Conan Doyle, Mark Gatiss and Steven Moffat. I only own the plot changes.

**Authors Notes: **Well, here it is! If you like it, send me a review! If you don't like it, send me a review! Just review, I love constructive criticism!

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><p>Doctor Molly Hooper was a perfectly normal English woman. Her appearance was average, with light brown hair and a thin body which she kept dressed in comfortable clothes, if not always stylish. She had a full-time job at St. Bart's as a pathologist, which she absolutely loved. Her Pomeranian named Toby kept her company in her small flat. It was just her human friends who were not-so-normal, if she could call them "friends." John Watson was quite nice to her when they occasionally passed each other in St. Bart's while on a case. But Sherlock Holmes, Consulting Detective, was a whole different story.<p>

Her feelings toward him were quite obvious to all others, with the exception of the man on the receiving end. Molly wasn't even sure if he had ever had any feelings for a woman. Or any person, excluding his friend John. However, the friendship between Molly and Sherlock would suddenly become tested, unknown to both parties involved.

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><p>"Hey Molly, I'm heading out. You should think about doing the same." Her co-worker poked her head into the morgue, seeing Molly sitting at her cluttered desk, chewing on the pen cap. "You've been working a bit later than usual."<p>

"Oh, yeah. I'm almost done here." She put her pen down and faced her friend, throwing her a friendly smile. "I've just been finishing up with some paperwork. I'll be through in a minute."

"Well, if you need help, just call." Audrey offered with a smile. "Night, Molly."

After a while, the sun started to set. Molly put her head in her hands and heaved a big sigh, looking at all the work she had to complete over the weekend. She had been working late at St. Barts all week and couldn't wait to go home. She packed up her things in a hurry, shoving odds and ends into her small messenger bag. Slinging her work-filled tote over her shoulder, she flicked the lights off and headed towards the door. It was locked.

"Hmm." Audrey had probably flicked the lock on her way out. Molly reached into her bag and shuffled around for her keys, freezing when she heard a voice.

"Hello, Molly." Her heart skipped a beat and she whipped around as her bag slid to the floor, blindly searching for the intruder. The menacing, unfamiliar voice spoke from the back of the morgue. "Fancy meeting you here."

Molly stuttered, breathing heavily. "Wh-What are you doing here? Who are you?"

"Oh, I'm just...passing through. I'm a friend of Sherlock's." His voice got closer and closer to Molly, circling her. "How is he? Have you seen him lately?" The man's voice was getting closer.

"Uh, I-I dunno. What do you want from me?" Molly crept away from the voice in the darkness. Hands shaking, she tried the other door, but it was locked too.

"Oh, Molly Hooper. I don't need anything from you." Molly fished around in her pockets for her cellphone, coming up empty. It was in the bag she had dropped by the door. Her escape options were becoming more limited. She could feel herself getting desperate and breathing more heavily, her heart pounding in her ears.

"Then wh-why are you-" Molly stuttered nervously.

"Oh, I'm just doing an experiment. It involves you...and Sherlock."

Molly perked up, still avoiding the stranger in the dark as best she could. She was trying to buy time to find her keys, or at least a weapon. "Sherlock? Why would you want him?"

"Well, now that Jim's dead and gone, I'm in charge. And I don't think I'm quite finished with him yet." He was associated with Jim?

He suddenly grabbed her firmly around the waist and held her against his body."I want to break him. Starting with you."

Molly gasped, realizing his intentions and struggled to break his grip from her wrist and back. Her blood raced, her pulse pounding in her ears. Molly screamed. She hit his chest over and over with her hands. She kicked his legs wildly with her feet. That only seemed to make him angry, and he slapped her harshly across the face. She fell to the floor, landing on her arm.

Gasping in pain, she tried to crawl away. The man kicked her straight in the side, her body slamming into a filing cabinet, pain shooting across her torso. Molly had no time to recover and gather her senses before he snarled and pinned her hips between his man ripped her button-down blouse down the front. Buttons flew all over. Crying, she squirmed under him and screamed at him to let her up.

"Let's just see how much it takes to make you break."

Molly screamed.

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><p>She woke with a start. It was completely dark in the morgue, the bitter smell of blood permeating the air. The memory of being violated rushed back to her. Molly began to breathe heavily as she looked over herself. Her clothes were in tatters, side and midsection were aching. She felt her shoulder and decided that it was broken, a pained gasp exiting from her. Molly sat up slowly and looked down, seeing blood stains smeared between her thighs. This caused her to scream loudly, and she heard knocking on the morgue door.<p>

"Molly?" The voice was deep and familiar, making her cry even more. She heard him trying the door, but it was still locked.

"Lestrade? Help me! Help me, please!"

"I'm breaking the door, Molly, brace yourself!" She leaned up against the wall while the Detective Inspector shot the lock. He turned on the lights and raced in. Lestrade knelt next to her and looked over her quickly, eyes widening. "Molly, who did this to you?"

She shook her head, tears streaming down her face. "I don't know, please just help me."

"Okay, I'm going to go get a nurse to help you, Molly. I'm not leaving, I will be right back, I'm only going into the hall." She closed her eyes and nodded, trying to get her sobbing under control, but not being able to. He touched her face gently before jumping up and running toward the door. "You! Get over here! An employee's been assaulted!" Molly heard two pairs of footsteps running toward her.

"Oh god, Molly." Her eyes flew open as she took in the sight of John Watson with a shocked look on his face.

"Help me, please," she whimpered. His hands slid underneath her frail body and lifted her into his arms gently. "Molly, I'm going to take you to the emergency ward. Just hold tight, I'm going to help you." Molly turned her head into his shoulder, staining his jumper with her seemingly-endless flood of tears and hiccups. She felt him racing through the brightly-lit hallways. Peeking outside a nearby window, she could see that it was still dark.

All she remembered before blacking out for the second time that night was the slight back-and-forth motion her body made as John ran quickly but carefully through the sterile hallways of St. Barts.


	2. Chapter 2

**A/N: I am blown away by the response of this story! Thank you all so much for reading and reviewing this story! You all keep me going! Enjoy chapter two!**

**A/N Part 2: I'm so sorry for the inconvenience, but some of the chapter didn't upload so I'm uploading it again. So sorry!**

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><p>Beep beep. Beep beep. Beep beep. Beep beep.<p>

This was the first thing Molly noticed as she slowly opened her eyes. Obviously she was still in the hospital, the beeping machine hooked up to her arm. The sterile smell of her room invaded her nose and combined with the brightness, spurred on a splitting headache.

The second thing she noticed was the pain. Her entire torso felt like she was run over by a truck. She reached up and felt her head, wincing in pain when her fingers found stitches. Molly surveyed the rest of her body with her hands, feeling bandages around her ribs. It crinkled as she stirred - feeling wrong, feeling empty. A large part of her was gone. She wasn't quite sure what part exactly. Her security? Her faith in goodness? It was shattered. Molly tried leaning up, but was stopped by a pair of hands.

"Take it easy, love. You're safe now." A feminine voice spoke gently, smoothing back her hair. "I'm your nurse. Will you tell me how you're feeling?"

She shook her head. "I have no idea." Molly choked, tearing up. She shifted a small bit, testing her broken body. Molly felt abused, exposed, and completely naked, despite the fact that she was clothed. She didn't feel quite human, all the good parts of her had been taken away. She didn't know who she was anymore. She didn't know how she felt. "I'm not sure how this could have happened."

"Hey, hey love," the nurse replied, stroking her hair as Molly started to shake with sobs. "You're safe, you're safe. Your injuries were quite something though. We gave you 6 stitches on your head, wrapped up some bruised ribs, and gave you some painkillers for that shoulder of yours. We are going to take good care of you, love." Molly let her tears fall down her cheeks as the friendly nurse held her hand, rubbing soothing circles on her knuckles. After a few moments, she spoke again. "Molly, the detectives would like to know what happened. Will you speak with them?"

She nodded, and the friendly nurse patted her cheek softly before leaving her room to get the detectives. Molly tried to smooth out her hair before someone saw her in that state, glancing down at her body. It was covered in a hospital gown, a plain white blanket up to her waist with her right arm in a sling and bandages wrapped around her middle.

What now? She had no idea of the answer. Molly was beyond scared. Tears still rolling down her cheeks, she swiped them away fiercely as the creaking sound of the door interrupted her. Lestrade was at the door.

"God Molly, its good to see you awake. How are you feeling?" He asked as he moved toward her bedside and sat at the small chair next to the bed.

Shrugging her shoulders, she answered in a small whisper, "I have no idea, really. I'm hurt and I'm scared. I don't know what to do." Greg gave her a soft, sympathetic pat on the hand. "How long have I been asleep?"

"About half a day." She shuddered, and winced at the movement as Lestrade went on. "Molly, if you're feeling up for it, we would like to know what happened. Would you tell me?" She gave him a nod and slowly started to recall everything as the DI reached into his back pocket to retrieve his pen and notepad.

"I was working late, and the sun had started to go down. I packed up my work and got ready to leave. But the door was locked." She let out a nervous chuckle. "I thought nothing of it- only that maybe my co-worker Audrey had accidentally flipped the lock after she visited me. But then I heard a voice from the back. I tried to get away, but I-" Molly choked up. "I couldn't. The man cornered me. I had no place to escape. Then he pushed me down and kicked me in the side. And then he-" Molly choked. "He took advantage of me." Lestrade set his paper pad on his knee and held Molly's hand, muttering reassuring words.

"We can do this some other time-"

"No." She replied harshly, fighting tears. "I want to figure this out. I want to find who did this to me."

"Okay." Lestrade sighed and continued. "Did you see him? Can you tell me what he looks like?"

"No, I had turned the lights out before I went to lock the door. I never saw his face."

"Could you recognize his voice?"

"Never heard it before, but I could pick it out if I had to. It was quite deep sounding."

"Did he tell you anything?"

"Yes, he talked at me for a while. The intruder said that this was an experiment. He said-" Molly paused, remembering a vital piece of information. She gasped, covering her mouth with her hand. "Oh, god. He said that now Jim was gone, he was in charge." Greg's neck whipped up, eyes widening in fear. "And he said that...he wanted to break Sherlock."

"Jesus." He jumped up quickly and reached into his back pocket. "Molly, I'm going to call him and tell him to come in. Sherlock will want to talk to you, do you think you can put up with him for a few minutes?" Molly nodded and the Detective Inspector scuttled into the hallway, dialing his number and holding the door for her nurse as she walked back in to check on her patient.

"Molly, would you like something to drink?" she asked while checking her vitals and adjusting her IV. "Or possibly a small something to eat? You could nibble some crackers?"

"No, thanks. I don't think I can stomach anything at the moment. What did you say your name was again?" she asked shyly.

"Oh, sorry. My name is Mary. Mary Morstan."

Mary shook her hand as Lestrade opened the door.

"John and Sherlock are on their way, Molly."


	3. Chapter 3

**A/N: Sorry it took so long to update! I've been struggling to find time to write. Please read and review! Thank you!**

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><p>The room was too quiet. The heartbeat monitor, the ticking clock, it was not enough noise for Molly Hooper. Noise was good, she didn't want to be alone with her thoughts. To be honest, Molly wasn't quite sure how to react. She was shocked and scared, of course. She was angry and confused. All of these emotions were locked up in her broken body bursting to get out. She didn't know what to do.<p>

"Would you like some more painkillers, dear?" Mary asked kindly, thankfully interrupting her train of thought. Molly sat up a bit to test her wounds, but winced painfully and nodded.

"Thought as 're looking a bit...not good."

"I don't mean to be rude, but why are you being so nice to me? I mean, you've been very kind to me, and I appreciate it very much, but you can't be this way with all your patients. So, why me?"

Mary sighed. "I've been in your shoes, darling, I know what it's like."

Molly was stunned. "You-you've been...raped?"

Mary nodded somberly and sat at her bedside. "Yes. It happened when I was a teenager. One of my friend's exes. He came on to me when he was drunk and just wouldn't take no for an answer."

"So, what happened afterwards?"

"Well, I pressed charges. He was put in jail for quite some time."

Molly hesitated. "How did you -y'know- take care of yourself after that? How did you become...better?"

Mary waited a bit before answering, "I decided that I didn't want my life ruined by this monster. I decided that I didn't want to be scared anymore. I didn't want to be helpless. And it took a while, when I didn't have to constantly look behind my shoulder anymore. I still do look, and I suppose I will always be scared, but I've learned that being scared is a part of life, and I have to make it not such a big part anymore."

Molly was in tears. "I just wish I could know what to feel. I'm so angry and scared and shocked, I don't know what to do. I don't know what I'm going to do once I get out of here."

Mary stroked her hair gently. "You try to go back to normal. And that's all you can do."

Nodding in understanding, Molly sniffled and Mary handed her a tissue.

They both sat in quiet silence, when the door opened and Sherlock's long frame quickly appeared, John right behind him.

He looked the same as he always did. Pressed clothes, blue scarf folded around his neck and a long coat molded into his frame. The only thing off was his countenance. Sherlock's face was devoid of emotion, maybe a bit too blank. His hair was ruffled, and his eyes looked tired as they stared sharply at Molly's face. She ducked her head and tucked her hair behind her eyes, embarrassed at his blatantly obvious stare.

"Hello, John." Mary said quietly. John moved and went to give Mary a kiss on the cheek. Molly raised her eyebrows and Mary blushed. John didn't notice and spoke up.

"Mary, I see you met Molly. How are you?" He held Molly's hand for a moment as he looked into her eyes seriously.

Molly wiped some tears away and said "I've been better, I think. I'm very sore and confused. And thank you for helping me, by the way. Thank you so much, I don't know what would have happened if you hadn't been walking by." Molly reached out her arms to John and gave him a warm hug.

"Don't think on it, anyone would have done the same." He smiled warmly at Molly and kissed her forehead. "I'm glad you weren't hurt any more seriously than you already are."

Sherlock finally piped up for the first time since he got to her room. "Yes, well, now that all these pleasantries have been exchanged, could we get down to business please?" He occupied the seat next to Molly's bed and leaned forward, elbows on knees and fingers under chin. "Molly, you said that your attacker was Moriarty's replacement. Did he say anything else?"

"He said he was doing an experiment. He said it involved me and you, and that he wanted to 'break you.'"

Sherlock blinked, keeping his blank expression. "What did he look like?"

"I have no idea. The lights were out, I never saw him."

He thought for a moment before speaking. "Molly, I know this experience has been hard, painful, and emotionally traumatic, but I'm going to need to examine your injuries."

"Now wait just a minute," Mary said and moved quickly between Sherlock and Molly. "You will do no such thing."

He stared Mary straight in the eye with a sudden fierceness and moved closer. "If I can observe Molly's injuries, I could figure out the attacker's height, weight, and possibly his purpose for attacking Molly. I gather the information, give the facts to Mycroft, he can send out hundreds upon hundreds of men to look day and night for him. And I can assure you, Mary, I will not rest until this attacker is found and punished. Now, will you allow me to do Molly justice, or will you stand in my way?" The fire in his eyes had spread to his face.

Molly spoke up. "I will let you, Sherlock. I trust you, and I just want the bastard to be found." She looked at Sherlock. "I know you can find him. Please, just help me. I want him gone."

He nodded, and turned towards Mary. "If you are worried about my intentions, you may stay here."

"You bet your arse I'm staying here. John, out. Molly needs to keep at least some of her innocence." John walked out the door of the over-cramped room and muttered about getting some coffees.

"Okay," Molly breathed. "Let's get this over with." She sat up and threw the thin hospital blanket off of her body. Mary reached behind Molly's back and untied the laces on her gown, pausing to look at her face for permission. She nodded and carefully slid her arm out of the sling, wincing at the movement. Mary held her arm in position as she slowly slid down her gown to reveal her nude body.

Molly couldn't believe how disgusting she looked. Her body was completely battered. Purple bruises peeked out of the bandages from her ribcage and surrounded her breasts and thighs. Finger-shaped marks wrapped around her biceps. Red crescents marked the skin at her hips where her attacker had dug his fingernails into her. She was used. She was ugly.

She glanced at Sherlock's face. It was utterly and completely blank, infuriatingly so. He had been so calm and gentle with his voice ever since he arrived. The only thing that betrayed his unfeeling face was his eyes. They were burning with hatred and rage as they surveyed her carefully.

Sherlock finally spoke. "He is six foot four exactly, 68 kilos with a bulky build. The bruises are set in such a way that he can only be a foot taller than Molly, and a good 10 kilos heavier. The purpose is unknown, however, I will talk to Lestrade about seeing her ruined clothes. I suspect they are still here somewhere which should give me everything I need to know. I will find your attacker relatively soon. In the meantime, you shall need to stay with someone who can watch over you until he is incarcerated; therefore, I have arranged for you to stay with Mrs. Hudson as soon as you are released. You personal belongings will be there for you along with your annoying dog."

He talked a mile a minute as he gently helped Mary pull up Molly's gown and replace her sling. He became quiet for a moment and said "Thank you Molly, you've been extraordinarily brave." Sherlock kissed her forehead quickly and walked confidently out of the door.


	4. Chapter 4

**A/N: Thank you so much for waiting patiently for a new chapter! I will try to update once a week. Please read and review!**

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><p>"Okay, Molly, I think we are ready for you to get out of here." Mary jotted a few last things down on the clipboard at the foot of her bed before handing it to a different nurse. "We really must go out for drinks sometime, okay?" Molly agreed, and the two girls smiled at each other. She and Mary had become good friends over the few days, after she had realized that Mary was John's girlfriend. No wonder she had been so well taken care of. It was a good thing that so many of her friends were in higher places.<p>

Mary carefully settled Molly into a wheelchair and rolled her down into the St. Bart's lobby. She was kept in the hospital overnight to make sure that her pain had gone down. She didn't mind very much, but as it had been a day and a half of uncomfortable and invasive procedures and questions, Molly was keen to get home. Not that she could actually go to her own home. Sherlock had arranged for her to stay with Mrs. Hudson while he tracked down her attacker. Molly was fond of Mrs. Hudson, so it wasn't as unbearable. She did very much want to just go home, but she supposed it was for the best.

The doors to the outside of the hospital slid open, and John stood there with a freshly hailed cab. He was to escort her back to 221B, and by the looks of the luggage-filled trunk he had already stopped by her place to retrieve some of her clothes, personal items, and Toby.

Mary placed her hand gently behind Molly's waist and hoisted her up off the chair. They quickly exchanged a friendly hug and Molly gave Mary her sincerest thanks for everything she had done to help her. John gave his girlfriend a kiss on the cheek as he took Mary's place and helped Molly into the cab. He slowly sat her down and buckled her seatbelt, as her sling restricted most movements of her dominant arm. John scurried into the car and ordered the driver off to Baker Street.

The ride was filled mostly with chit chat. Molly asked about his relationship with Mary and teased him on why she hadn't met her before now. After a while, Molly became quite sore from the bumps and jerks of the cab, so she and John quieted for a small while. Leaning her head on the side panel, she gazed out the window. Everything looked so normal. How could that be when her whole world had recently been toppled upside down? "Time waits for nobody," Molly supposed. "It just keeps going. Time doesn't have setbacks like humans. It's not even a real thing, yet it's godlier than humans."

A few moments later, the cabbie stopped the car at the front door of 221B Baker Street. John threw some bills at the driver and stepped out of the car, rushing to help unbuckle Molly like a gentleman. Suddenly, a sleek black car pulled up behind the cab. Some strange men in nice suits jumped out and headed toward them, making Molly nervous. She shuffled a bit behind John for some distance.

Noticing her discomfort, he turned around and said, "It's okay, Molly, it's just Sherlock's brother Mycroft. He likes to make dramatic entrances. Though I'm not entirely sure why he's here." She breathed a sigh and stared at the older man making his way towards them. He looked forty-something with a beautifully tailored suit and an old yet friendly complexion.

"Hello, John. Molly." He gave them both a short nod. "Considering that there's only one person around here that's not ill of health, I have brought some people to help move your belongings into this barely adequate residence. I extend my deepest sympathies to you, Molly, for your unfortunate experience. I will, of course, pay the rent for your vacant apartment during your stay here." He smiled a bit at her before moving past them to direct his men into Mrs. Hudson's apartment.

Molly looked back at Sherlock's older brother with wide eyes, hardly comprehending their one-ended conversation. Who in the world would waltz up and insist on paying for her flat? She didn't get much time to think on it, as John urged her inside. "Let's get you resting." She and John entered the building and made their way towards 221A. Molly knocked sharply on the door, and the sounds made her head pulsate. John was right, I need to take it easy. And maybe take some pain pills.

After a few moments, Molly knocked again. "Mrs. Hudson?" she asked shyly. There was no reply. John knocked a bit louder. She was an older lady after all; her hearing was probably not as keen as it used to be.

A thundering noise rolled down the steps, and Sherlock stood before them, handsome as ever with his coat and scarf on. Disregarding Molly and John completely, he strolled past them.

"Sherlock, where's Mrs. Hudson? Is she upstairs?"

The Consulting Detective stopped short and turned around, facing the two. "Mrs. Hudson has been called away from Baker Street. Her sister has fallen ill; seeing as the door isn't locked and she left her scarf sitting on the ground here, she was in rather of a hurry-possibly in distress." The silky lavender scarf lay on the ground. He picked it up and folded it into his coat pocket. "I would say by the hurry of the lady in question her sister is ill with the flu and possibly dying. We shall see when she returns or calls; I estimate she will phone in one week time." Sherlock suddenly turned around and walked toward the door again.

"But Sherlock, Molly was supposed to stay with Mrs. Hudson, she can't stay by herself." John walked over to him and grabbed his arm. "Where is she supposed to go now?"

He glared at John with a look in his eyes. "Isn't it obvious? Molly is to stay with us. She will take my room, seeing as I hardly sleep anyway. I shall make do on the couch." The best friends looked at Molly, who was standing with confusion plain on her face. She looked a bit sick. Sherlock walked over to Molly and stared at her face as if to figure out what was running through her mind.

"Molly Hooper, welcome to 221B."


	5. Chapter 5

**A/N: Here's your new chapter! Please review!**

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><p>Molly sat stunned on the couch as Mycroft's men carried her things up the stairs and into Sherlock's bedroom. She was prepared for a quiet few weeks with her elderly friend, not a few weeks of loud noises, quick deductions and awkward encounters. The changes were so sudden, it made her head spin.<p>

She wandered into the kitchen and peeked in the cabinets, looking for a glass so she could take some much-needed pain medication. As she glanced in the wood cupboards, Molly noticed that there wasn't a lot of food. Some ceramic bowls and plates, mugs and a tea set were the best things she could find. Some others were jars of murky unknown liquids which made Molly's stomach turn. Finally, she reached for a mug and filled it with tap water from the sink and downed her pills.

Her body was still in a lot of pain, so Molly decided to rest on the couch for a while. Grabbing a nearby pillow and a blanket, she laid down on the couch, minding her shoulder. She had no idea where Sherlock and his partner were. John took her upstairs while Sherlock stayed behind, possibly to talk to his brother. Her eyes drifted shut as her pills began to kick in.

_"Shut up! Shut up!" a voice screamed at her. She ignored him and yelled at him, begging for him to stop running his hands all over her, hurting her. He grabbed her long hair in his hands and slammed her head on the cold tile floor. "I said shut up!" He was furious. _

_Molly gasped as her head flooded with pain. The intruder presses his hips against hers, licking the side of her face. She tried squirming away from him in vain. He ripped her trousers with his hands and sneered at her. "You are a worthless bitch." He slapped her face viciously. Molly could feel the blood dripping out of her head and her nose, pooling on the floor. _

_She groaned and screamed for help, screamed and screamed. But nobody could hear her, it was useless. Another harsh slap and everything became black. _

She jerked awake, still in 221B, still on their couch, thank god. Her legs were thrashing, tangled in the blanket. Breathing heavily, Molly sat up quickly and looked around the room. The boys weren't there. She released a shaky breath and held her hands over her eyes, trying to get a hold of herself. Molly sat in a fetal position and shook with seemingly endless sobs. Tears raced down her cheeks. She didn't know how to make them stop.

"Molly?" Her fuzzy head snapped over to the voice. Sherlock was standing in the doorway. He stepped a bit closer to the hysterical woman on his couch. "What happened?"

She didn't answer and instead scooted off the couch, throwing the blanket off of her sweaty body and wobbled over to the water mug she used earlier. With shaking hands, she lifted it to her lips and took a small drink, trying to calm herself.

Sherlock, still standing by the doorway, slowly walked over to the frightened woman in his kitchen. He put his hands over hers and gently took the mug and set it on the table. Looking back at her, he noticed her scared eyes and tear tracks. "Did somebody hurt you?"

She shook her head no. "I-I just had a dream. A nightmare. It was awful, Sherlock. Awful." Her body shook with sobs while he looked on. "I don't know what I'm going to do. How can I even sleep when he's-" She collapsed on the floor in a heap, covering her eyes in shame.

After a moment, he sat down on the floor next to her. "I can't pretend to understand what you've been through. I can't pretend to understand how it felt to have been violated in such a way. However, I will do the only thing I can think of. That is to say, find that monster that did this to you." He stared at Molly gently. "And I will, I will find him. I promise." Sherlock moved in front of her and took her hands in his, pulling her up from the floor. Molly leaned into him, and he awkwardly wrapped his arm around her slim shoulders. He held her as Molly continued to cry into his coat.

After a few moments, she calmed down and pulled away. "I'm sorry about your coat," she apologized, sniffling. Sherlock smiled a small bit.

"Don't think anything of it." They both stood in the kitchen looking at each other until Molly finally excused herself to settle into his room.

Walking slowly down the hallway, she observed everything she could about their apartment. It was quite small and scientific. The walls were a pukeish green, no picture frames. There wasn't anything sentimental in their apartment, which wasn't very surprising. Molly reached the door to Sherlock's bedroom and slowly turned the knob.

Sherlock's room was a bit obvious. Several bookcases lined the walls, filled to the edges with well-used literature. The wallpaper matched the living area and a framed periodic table sat near the door. Everything was clean and orderly, not a speck of dirt anywhere. Surely Mrs. Hudson didn't come in here, so Sherlock must be a bit anal about his things.

Molly staggered to the large bed, her luggage bags sitting near her. She didn't really have the energy to unpack so she unzipped one and rooted around, finding a baggy t-shirt. Mary told her that she was supposed to get help while changing and showering, but there was no way in hell she would ask Sherlock to assist her. Molly's cheeks reddened just thinking about it. She was a doctor; she could handle a healing dislocated shoulder.

Holding her arm carefully, she maneuvered her sling off and then her shirt. Taking a hold of the fresh one, Molly put her wounded arm in first and then carefully pulled the fabric over her head, careful of the stitches. When she was finally settled, Molly felt tired from the day and went to take a rest, even though she tried to deny her lack of strength. She lifted up Sherlock's bedspread and settled into the soft mattress. It smelled like him.

Keeping her eyes open until the last moment, she tried to make herself as tired as possible before eventually drifting off to sleep. Maybe she wouldn't dream tonight.


	6. Chapter 6

**A/N: I'm sorry about the delay, but here is chapter 6 at last! I have planned out most of the story in my time, I haven't just been lollygagging about with this! **

**And starting now, as a desperate and blatant attempt to get more reviews, whoever writes one will get a sneak peek of the next one! **

**So, as always, read and review! Thanks!**

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><p>It was a soft knock that woke Molly up. She hadn't had any nightmares, thank god. Staying up as late as possible seemed to do the trick, but the downside was that Molly was completely exhausted. Sighing, she murmured a "Come in" to the knocker and sat up, tiredly rubbing her eyes.<p>

John slowly opened the door quietly. "Molly, I've got breakfast made if you're up for it. Nothing fancy, just some eggs and toast." Thinking at how she hadn't eaten much in the past few days, she decided that a little food wouldn't hurt, and told him that she would be out in a minute. John closed the door again and left Molly to dress.

Her aching shoulder and ribs screamed in pain at the lack of pain meds. She decided to change clothes once she had something to deal with the discomfort. Molly threw a dressing gown over her pajamas and slowly made her way into the kitchen, mindful of her injuries.

The smell was heavenly, and Molly soon realized just how hungry she was. John set a plate of fluffy eggs and buttered toast on the table with a pill and a water glass. "Thought you might need this."

She nodded in thanks and took a seat at the table. Throwing back her head, Molly threw the bitter-tasting pill in her mouth and quickly downed it with a glass of water. Immediately, she tucked into her eggs. John made a plate and settled in the chair opposite her. They pair ate in an awkward sort of silence until John decided to break it.

"So, what are your plans for today, Molly?" John asked while he sipped coffee.

"I'm not quite sure. Maybe read a book? Tidy up a bit?" She answered vaguely. "I don't really fancy sitting here doing nothing while you two are out and about."

"Molly, you don't have to clean, you should be resting, trying to get better."

"I won't be up long." Molly said, scooping bits of scrambled egg into her spoon. Just then, her phone buzzed. _David Hooper_ flashed on the screen. "Oh, gosh. I'd better take this." She sat up from the chair and walked toward Sherlock's room, pressing the phone to her ear.

"Hi, David." Molly said shyly. She had meant to call him sooner, but the past few days had been a whirlwind. "I'm so sorry, I should have called." She was interrupted by her big brother's voice.

"Oh god Molly, I'm so glad that you're alive. I've been worried sick about you."

Molly closed the door slightly and wandered over to the window. Parting the curtains, she looked out at the dreary grey morning clouds. "I know, and I'm very sorry I haven't called earlier. It's been a rough few days." Molly stared out Sherlock's window, leaning her hip on the windowsill. She listened idly as David said the typical condolences of people who really didn't understand what her situation was like. She appreciated the thoughts and love though.

David finally spit out what he had wanted to say from the start. "Molls, I have to say, I really worry about your safety, and I think it's best for you to come back home to Blackpool."

Molly's mouth dropped open in shock. _Move back home? _She had thought about it a few times, of course. After their parents had died, David was all by himself. She almost moved back to be with him, but suddenly got a job offer from St. Bart's, one that she definitely could not refuse. But would she be able to move back now? So many things had changed. She had friends, a job that she loved more than anything, a small flat, Sherlock. She couldn't leave Sherlock. He may not feel the same way about her, but she did love his genius and tender heart hidden underneath all his robot-like personality.

"Molls? Are you there?" David's soothing voice brought her back to reality.

"Yeah, David. I'm here."

"So, will you? Move back here, I mean? I have an extra room here at the house; you could stay for a while until you got back up on your feet. I could protect you, Molly."He sounded so hopeful. David was lonely too, she could feel it. But she couldn't accept.

"No, I can't go back. I have friends here, my dream job too. I can't up and leave." Molly said softly. "Besides, I'm staying with friends. They are taking very good care of me." She glanced toward the door as if John could see her. "They're detectives. And they're going to find out who did this to me."

David was quiet for a long while. "I still think you should move back," he whispered.

There was a sudden crash in the living room. Molly nearly jumped out of her skin and ran toward the sound. "David, I have to go. I love you, and I'll talk to you later. Bye." She hung up before he had a chance to respond, and whipped open the door and dashed down the hall to see Toby, her Pomeranian, up on the counter with a silly grin on his face and a smashed glass on the ground.

"Toby, you bad boy!" Molly quickly rushed over to the counter and scooped him up into her arms. Thankfully, neither John nor Sherlock were anywhere to be seen. He licked her face affectionately. "That was not very nice, we are guests after all." She walked him over to his crate and settled him gently into it, giving her a chance to pick up the mess left behind.

She grabbed a rag and a dustpan, and crouching down (trying not to groan in pain), brushed the broken glass into the bin. It wasn't until she turned around that she realized that she was not alone. Sherlock stood behind her; coat, scarf and all.

Molly jumped a bit, but wasn't as scared when she realized who it was. His hair was unkempt, his coat was crumpled, and his breathing was a bit more rushed than usual. He was probably out early, running around and hadn't had time to take a shower.

"How are you today, Molly?" He asked in his deep voice, the one which she had loved from the start.

"Fine, I guess. Still a bit sore." She motioned toward the rubbish bin. "Sorry about the glass, by the way. I will pay for a new one after I-"

"Don't worry about it," Sherlock cut her off. "It's only a glass, after all."

He was acting sort of strange. "Have you figured anything out? About my-my attacker?" Molly asked hopefully, wringing her hands in front of her.

Sherlock shook his head slightly. "No, we haven't found him yet. We will keep looking, I promise." Softly touching her face with his fingertips, he gently traced a bruise. Almost as soon as he had touched her, Sherlock removed his hand and waltzed over to his chair, picking up his violin and softly playing a song.

Since she had nothing else to do, Molly took a seat on the couch near the door of 221B and listened to Sherlock play his melody, weaving throughout the silent apartment.


	7. Chapter 7

**A/N: Long time, no see! Thanks for sticking by me and this story, beautiful followers!**

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><p>Sherlock had been playing his violin for the good part of half an hour. It was fascinating, watching his lithe fingers coax a tune from his well-used violin. His face was blank and his eyes closed while he minutely swayed his hips to the rhythm. Molly closed her eyes to better listen to the song. It was slow, yet mournful.<p>

Sudden footsteps ascending the stairs broke Molly's reverie. She glanced towards the door as John and Mary entered the apartment.

"Molly dear, how are you?" Mary walked towards the couch as Molly stood up to hug her gently.

"I'm okay, I think. Still sore, but that will go away, I'm sure." They both stepped back, breaking their embrace. Mary was dressed in light clothes and her short blonde hair was slicked back. She must have been let off the long shift at St. Barts. Mary did look tired, so she walked her over to the couch and sat them both down. "What brings you here?"

"Oh, you know, I wanted to check up on you. I only just got off work and thought I might lend a hand with a bath, and I didn't think that you'd want the boys to help you." They both glanced at Sherlock, who had since put down his violin and sank into his chair, fingers under his chin as was his signature move while thinking.

Molly smiled warmly at Mary. "Oh please, that would be lovely. I'm starting to smell." They both giggled and walked toward the bathroom.

John sighed and walked over the chair opposite Sherlock, looking at him. He waited until the girls were out of earshot before saying anything. "Did you find something from Molly's clothes this morning?"

Sherlock rubbed his temples sharply with his hands. "No, there wasn't a single hair, clothing fibre, blood molecule or bodily fluid. This man was smart to leave no evidence; we're dealing with a professional, quite possibly an enemy out for revenge." He jumped up and paced back and forth, the only noises were of John's breathing and the faint trickle of the tub faucet running.

"Well, what about the tests they ran on Molly?"

"They won't let me see the results or data." The pacing continued. "I've spoken with several nurses and doctors, all of which know my name, but none of them will let me inspect the evidence."

"And what about the morgue?" John asked.

"Also nothing, the rapist cleaned up after himself, most likely while Molly was still unconscious." His pacing increased, as did his voice. "Knowing that, this attack must have been planned out with precision, waiting until all the tools were acquired and the situation correct. He must have been watching her for quite some time, waiting to strike; therefore, he probably lived or worked near the morgue where he could easily be within eyeshot."

"So," John said harshly, "You're telling me that we have nothing. I know she may not be all that important to you, Sherlock, but Molly is one of my good friends. I would have expected you to put a little more effort into this one."

The Consulting Detective paused and turned to face his best friend. "What makes you think that I'm not trying? Besides, she's my friend too-"

"Friend?!" John jumped up and stomped towards Sherlock. "For God's sake Sherlock, you don't know what a friend is! I'm your only friend, and I barely tolerate you! _Bleeding Christ_." The detective's assistant shoved a hand through his grey hair and turned away. "What makes you think that you can be her friend? You only acknowledge her when you need a body part! Get a clue, Sherlock." John turned away and stormed towards his room, shutting the door firmly.

Sherlock stood frozen in the middle of the room, brows crinkled in confusion. He did care for Molly. Her safety was important to him, obviously, but there was also something else that Sherlock couldn't place. Molly was a pleasant person to be around, and always endured Sherlock's brusque insults. Her personality was quite charming; she was always nice to everybody, especially the Consulting Detective (though he didn't usually deserve it).

He began to pace again, deeply pondering any possibilities to Molly's case. He wanted the bastard to pay for what he did to Molly. Sherlock tossed his coat and scarf on and rushed out the apartment. His never-ending hunt for clues continued.

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><p>She sat on the edge of her bed with a ratty t-shirt on and some sweatpants. Mary kneeling behind her, rhythmically combing Molly's wet hair. The soft pulling motion was relaxing, and Molly felt herself nodding off.<p>

"Molly, is there anything I can help you with?" Mary questioned. She noticed that she had purplish bags under her eyes. Obviously she hadn't been sleeping well, and her muscles were tense.

"No, I don't think so."

Mary placed the comb on the bedside table and sat next to her friend. She placed her hand on Molly's and squeezed gently, looking into her eyes. "I know that nobody gets over an attack that quickly. It took me weeks to sleep through the night. I still have nightmares." Mary swept a lock of hair away from Molly's eyes. "You can always talk to me, Molly. Please know that. I really do want to help you."

Molly nodded, a tear rolling down her cheek. "I know. And you've been very helpful already. I just don't want to be scared anymore. It's exhausting." She sniffed. "He's always in my dreams, and I don't think he'll ever get out of them." She leaned her head on Mary's shoulder.

Mary stroked Molly's hair softly and held her while she cried.

"I can't tell you when it's going to get better. I can only tell you that it does. And one day, you are going to wake up and the sun will shine, and everything will be good again. It's like my dad used to say, 'Our greatest weakness lies in giving up.'"

Molly chuckled a bit. "That one was from Thomas Edison."

"Well I didn't say he made it up, did I?"

The two chuckled and Molly sent up a prayer for her real-life guardian angel. They sat together for a very long time and took comfort that they weren't alone. Molly thought of the others who, unlike her, didn't have a shoulder to cry on or a friend to comb their hair, and had to go through life alone. She never wanted to be without someone else.

Like Sherlock.


	8. Chapter 8

Molly bolted awake, breathing heavily. Nightmares still plagued her and it seemed unlikely they would let up anytime soon. She checked to see that nobody else was in the room with her, and then buried her head in her hands. No matter what she did to make herself sleepier, nothing ever helped protect her from the night terrors. Her attacker was always there. She rubbed her eyes and settled her breathing before slipping out of bed, throwing on a robe, and making her way to the kitchen.

She had been staying with John and Sherlock for almost a week now. They were good hosts, and Molly was terribly grateful for their company and protectiveness, but she was also keen to get back to her own home.

Shuffling quietly through the hallway and softly opening the cupboard, Molly grabbed a glass and filled it from the tap. It was around 3 in the morning. The only sounds were that of the clock ticking and the faint buzzing sound from the light above the table.

Suddenly, an arm grabbed her around the waist and pinned her to the countertop. Molly's heart sped up.

"Miss me?"

She immediately recognized his taunting voice. It was the rapist.

Molly prepared to scream, but he clapped his hand harshly over her mouth. "Now now, we can't have that." He rubbed his pelvis into her backside. Molly gasped and tried moving away, but he slammed her right back into the counter. "I don't think so." She could feel him becoming hard and she panicked as he laid his front against her back. Her attacker groaned and hungrily grasped her sleep pants in his hands, ripping them. He turned her around and shoved himself between her legs. She cried out and started fighting back against his touches, pushing him away.

_Where were John and Sherlock?_

Molly's rapist seemed to read her mind. "Ah yes, your protectors." He nuzzled his face against her neck. The intimacy of it made Molly want to vomit. "Want to see what I did to them?" He grabbed Molly by her waist and dragged her to John's room. She screamed and tried to kick out of his grasp, kneeing him right in the groin. This only caused him to become angry and grasp her tighter, forming new bruises. Kicking open John's room door with a snarl, he burst in and flipped on the light.

John was laying face up on his bed, his eyes open and his throat slit, bloodstains dripping into his bed sheets. A glazed faraway look was in his eyes. The good doctor, murdered. She was wordless. She couldn't breathe.

Beside him lay Sherlock. His beautiful blue eyes looked upward. His long throat was surrounded by wet red marks. She couldn't believe it.

She almost screamed. She almost passed out.

Her rapist dropped her on the floor and lay atop her. "You know, for a first-class detective duo, they were easy to kill. They didn't even scream." Once again, he shoved his face into her neck and bit her shoulder, making her bleed.

"Let's make you scream."

"Molly? Molly!" Her eyes snapped open and landed on the very man she thought was dead. Sherlock stared at her with concern plainly written in his face. "You were screaming, I-"

She threw herself into his arms, sobbing. "My god, you're alive." Grasping handfuls of his shirt, she buried her head into his chest. "I had such an awful nightmare." She felt his arms wrap hesitantly around her back and a hand settle behind her head.

"Yes, of course I'm alive, silly girl. Nobody can kill me without my permission." Molly chuckled wetly and sniffled, still upset at her night terror. He shifted them; him sitting on the bed, settling her in his lap.

"It was so real, so real…" Molly chanted breathlessly as Sherlock awkwardly rocked her back and forth. He wasn't really used to human contact, especially with a hysterical woman, but he tried his best.

He stroked her hair and whispered to her softly. "May I ask what happened?" Molly immediately stiffened.

After a while, she spoke. "He attacked me again. And he killed you and John." She doesn't know what made it happen, but all her feelings just spilled out of her. Her emotions and stress had been bottled up for days, and now it was all pouring out of her, like a faucet. "I just don't know what to do anymore. I'm so tired and I keep having these terrible dreams and I just want them to stop. I want to feel safe again, and I don't just mean being protected. I want to feel safe in my own body, like he's not going to suddenly show up in my mind like he always does." Her tears started up again. "Please just make him go away."

Sherlock was quiet for a long time, taking in everything and listening to what Molly had to say. He imagined what was going on in her mind, and here it was in front of him, his worst observations coming to light. Wiping her tears with his hand, he looked straight into her eyes. "I will help you, and I will do whatever it takes to make you better. You're my friend. Please trust me on this."

Molly sniffed and nodded her head. "I do. Trust you, I mean." She laid her head in the crook of his shoulder. "I trust you, Sherlock."

After awhile, Sherlock made to get up. "It's very late. You should try and get some more rest." He settled her into her bed and walked toward the door.

"Wait." Molly called out to him, his hand frozen on the doorknob, glancing back at her.

"Would-would you stay with me tonight? I mean, you don't really have to, but I just want to-"

He stripped off his shoes and socks, pushing them to the wall. Molly looked away bashfully while he unbuttoned his shirt and laid it haphazardly across a chair. Sherlock crawled under the covers and flicked off the lamp.

At first it was quite awkward. Molly lay there stiffly facing the ceiling as did Sherlock. However, as she drifted away, Molly felt the warmth of her detective's hand grasping her fingers, making sure that she knew, even in unconsciousness, that he was with her.


End file.
